In article <3ciijs$hjb at synapse.bms.com>, patel_p at bms.com (taylor) writes:
> Hi:
> I have the following two questions regarding the GAL4 DNA binding
> sequence:
>> 1) Is the following 18mer sequence the most optimal DNA binding sequence
> for GAL4:
>> 5'---CGGAAGACTCTCCTCCG---3'
In 1986 (EMBO J. vol 5, pg 603) we described 11 naturally occuring GAL4
sites which allowed the proposed consensus: CGGA(G/C)(G/C)AC(T/A)GT
(C/G)(C/G)TCCG. I don't know if others since then have found stronger
sites.
>> and
>> 2) If I were to make a synthetic binding site, and would like to arrange
> two binding sites in tandem, what is the optimal distance (# of bp) between
> the two sites.
>
Again, from natural selection in yeast, the high affinity GAL4 sites
upstream of four genes (in three UAS's) are 82 to 87 base pairs apart
(measured from centers of dyad symmetry.)
rick